Cellular Composition of Bovine Coccygeal Intervertebral Disks
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB44744 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR5896900.fastq.gz | Fastqsanger.gz | |||
| ERR5897760.fastq.gz | Fastqsanger.gz | |||
| ERR5896901.fastq.gz | Fastqsanger.gz | |||
| ERR5897761.fastq.gz | Fastqsanger.gz | |||
| ERR5896902.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:The aim of this transcription profiling study was to identify novel genes that could be used to distinguish bovine Nucleus pulposus (NP) cells from articular cartilage (AC) and annulus fibrosus (AF) cells and to further determine their expression in normal and degenerate human intervertebral disc (IVD). This study has identified a number of novel genes that characterise the bovine and human NP and IVD cell phenotypes and allows for discrimination between AC, AF and NP cells.<br><br>
2010-03-05 | E-MEXP-2291 | biostudies-arrayexpress
Project description:Intervertebral disc (IVD) is often the cause of low back pain. Degeneration occurs with age and is accompanied by extracellular matrix (ECM) depletion, culminating in nucleus pulpous (NP) extrusion and IVD destruction. Although the changes that occur with ageing in the IVD have been under study, not much attention has been given to ECM remodelling during normal development. Therefore, a thorough study of ECM composition and a comprehensive view on how this microenvironment is affected in normal ageing conditions is needed, to better understand the processes involved in IVD development and in age-associated degeneration. We have compared the NP matrisome of bovine IVDs from foetus, young and old animals by quantitative iTRAQ LC-MS/MS. Protein expression levels of the most interesting candidates were validated by Western Blot analysis. In total, 161 bovine proteins were identified. Of these, 77 molecules were common to the three different age groups, of which 36 defined the NP matrisome. Differential expression levels obtained for Collagen Type XI, XII, XIV, Fibronectin and Prolargin were independently confirmed. Herein, we demonstrate a shift in NP matrisome signatures that occurs in healthy bovine IVDs with development and ageing. Thus, this study provides insight into factors that may explain age-associated IVD degeneration, and which are putative targets for therapy. It also highlights key molecules, characteristic of early developmental stages, which constitute potential effectors in IVD regeneration.
2017-09-25 | PXD004922 | Pride
Project description:Very little is known about how intervertebral disc (IVD) is formed or maintained. Members of the TGF-ß superfamily are secreted signaling proteins that regulate many aspects of development including cellular differentiation. We recently showed that deletion of Tgfbr2 in Col2a expressing tissue results in alterations in development of IVD annulus fibrosus. The results suggested TGF-ß has an important role in regulating development of the axial skeleton, however, the mechanistic basis of TGF-ß action in these specialized joints is not known. One of the hurdles to understanding development of IVD is a lack of known markers. To identify genes that are enriched in the developing IVD and to begin to understand the mechanism of TGF-ß action in IVD development, we undertook a global analysis of gene expression comparing gene expression profiles in developing vertebrae and IVD. We also compared expression profiles in tissues from wild type and Tgfbr2 mutant mice. Lists of IVD and vertebrae enriched genes were generated. Expression patterns for several genes were verified either through in situ hybridization or literature/ database searches resulting in a list of genes that can be used as markers of IVD. Cluster analysis using genes listed under the Gene Ontology terms multicellular organism development and pattern specification indicated that mutant IVD more closely resembled vertebrae than wild type IVD. We propose TGF-ß has two functions in IVD development: 1) to prevent chondrocyte differentiation in the presumptive IVD and 2) to promote differentiation of annulus fibrosus from sclerotome. We have identified genes that are enriched in the IVD and regulated by TGF-ß that warrant further investigation as regulators of IVD development. Thirteen samples were analyzed. This includes three biological replicates of laser captured IVD from E13.5 day control mice, three biological replicates of laser captured vertebrae from the same E13.5 day control mice, three biological relicates of laser captured vertebrae from E13.5 day Col2aCre;Tgfbr2lox/lox mice, and four biological replicates of laser captured IVD from E13.5 day Col2aCre;Tgfbr2lox/lox mice.
2010-04-09 | E-GEOD-18647 | biostudies-arrayexpress
Project description:Intervertebral disc (IVD) degeneration is often the cause of low back pain. Degeneration occurs with age and is accompanied by extracellular matrix (ECM) depletion, culminating in nucleus pulpous (NP) extrusion and IVD destruction. The changes that occur in the disc with age have been under investigation. However, a thorough study of ECM remodelling is needed, to better understand IVD development and age-associated degeneration. As so, iTRAQ LC-MS/MS analysis of foetus, young and old bovine NPs, was used to define the NP matrisome. The enrichment of Collagen XII and XIV in foetus, Fibronectin and Prolargin in elder samples and Collagen XI in young ones was independently validated. This study provides the first matrisome database of healthy discs during development and ageing, which is key to determine the pathways and processes that maintain disc homeostasis. The factors identified may help to explain age-associated IVD degeneration or constitute putative effectors for disc regeneration.
2017-09-25 | PXD005616 | Pride
Project description:Objectives/Design: Intervertebral Disc (IVD) degeneration has been associated with a chronic inflammatory response, but knowledge on the contribution of distinct IVD cells, namely CD44, to the progression of IVD degeneration remains elusive. Material: Bovine nucleus pulposus (NP) cells. Treatment: Stimulation with IL-1beta (10ng/ml). Methods: CD44 NP cells were sorted and compared by gene expression and proteomics with the negative counterpart. Dynamics of CD44 gene and protein expression was analyzed upon pro-inflammatory treatment. Results: CD44 has a multidimensional functional role in IVD metabolism, ECM synthesis and production of neuropermissive factors. CD44 widespread expression in NP has been partially associated with CD14 and CD45, resulting in the identification of distinct cell subsets. Conclusions: This study points out CD44 and CD44-based cell subsets as relevant targets in the modulation of the IVD pro-inflammatory/degenerative cascade.
2024-05-22 | PXD048373 | Pride
Project description:Intervertebral disc (IVD) degeneration and its medical consequences is still one of the leading causes of morbidity worldwide. To support potential regenerative treatments for degenerated IVDs, we sought to deconvolute the cell composition of the nucleus pulposus (NP) and the annulus fibrosus (AF) of bovine intervertebral discs. Bovine calf tails have been extensively used in intervertebral disc research as a readily available source of NP and AF material from healthy and young IVDs. We used single-cell RNA sequencing (scRNAseq) coupled to bulk RNA sequencing (RNAseq) to unravel the cell populations in these two structures and analyze developmental changes across the rostrocaudal axis. By integrating the scRNAseq data with the bulk RNAseq data to stabilize the clustering results of our study, we identified 27 NP structure/tissue specific genes and 24 AF structure/tissue specific genes. From our scRNAseq results, we could deconvolute the heterogeneous cell populations in both the NP and the AF. In the NP, we detected a notochordal-like cell cluster and a progenitor stem cell cluster. In the AF, we detected a stem cell-like cluster, a cluster with a predominantly fibroblast-like phenotype and a potential endothelial progenitor cluster. Taken together, our results illustrate the cell phenotypic complexity of the AF and NP in the young bovine IVDs.
| S-EPMC8124861 | biostudies-literature
Project description:Very little is known about how intervertebral disc (IVD) is formed or maintained. Members of the TGF-ß superfamily are secreted signaling proteins that regulate many aspects of development including cellular differentiation. We recently showed that deletion of Tgfbr2 in Col2a expressing tissue results in alterations in development of IVD annulus fibrosus. The results suggested TGF-ß has an important role in regulating development of the axial skeleton, however, the mechanistic basis of TGF-ß action in these specialized joints is not known. One of the hurdles to understanding development of IVD is a lack of known markers. To identify genes that are enriched in the developing IVD and to begin to understand the mechanism of TGF-ß action in IVD development, we undertook a global analysis of gene expression comparing gene expression profiles in developing vertebrae and IVD. We also compared expression profiles in tissues from wild type and Tgfbr2 mutant mice. Lists of IVD and vertebrae enriched genes were generated. Expression patterns for several genes were verified either through in situ hybridization or literature/ database searches resulting in a list of genes that can be used as markers of IVD. Cluster analysis using genes listed under the Gene Ontology terms multicellular organism development and pattern specification indicated that mutant IVD more closely resembled vertebrae than wild type IVD. We propose TGF-ß has two functions in IVD development: 1) to prevent chondrocyte differentiation in the presumptive IVD and 2) to promote differentiation of annulus fibrosus from sclerotome. We have identified genes that are enriched in the IVD and regulated by TGF-ß that warrant further investigation as regulators of IVD development.
2010-04-09 | GSE18647 | GEO
Project description:Intervertebral disc (IVD) degeneration (IVDD) is a major contributor to chronic low back pain (LBP), representing a significant burden on the spinal healthcare system and a leading cause of long-term disability worldwide. Reliable in vitro models are lacking and thus monocultures of cell lines and 2D-based culture models are still used to study the patho-mechanisms of IVDD. We established functional multicellular IVD spheroid cultures using primary human annulus fibrosus (AF), nucleus pulposus and microglial cells. The IVD spheroid culture was observed to facilitate the IVD-specific phenotype and function. The spheroid culture markedly increased the expression of inflammatory mediators and chemokines in the presence of pro-inflammatory cytokines IL-1b, a master regulator of IVDD. Furthermore, we implemented our microfluidic chemotaxis platform to investigate microglial neuroinflammation in response to our reconstituted IVD spheroid models. Transcriptome sequencing revealed that microglia stimulated by potential contributing factors derived from IVDD spheroids exhibited a significant upregulation of chemotactic factors and cytokines including CCL2, 3, 4, 5, CXCL8, IL6, and IL1b (p < 0.05). Moreover, we observed considerable activation and infiltration of microglia induced by soluble factors derived from IVDD spheroids, which is expected to occur during IVDD. The chemotactic effects on microglia were reduced upon neutralization of CCL-2, IL-8 or inhibition of NF-kB signaling. These robust in vitro IVD spheroids can be used to model IVDD and provide a valuable platform for the assessment and development of IVDD therapeutics.
2025-12-25 | GSE278813 | GEO
Project description:Intervertebral disc (IVD) performs as a fibrocartilaginous joint to anchor adjacent vertebrae (VB) and is essential for the mechanical stabilization of axial skeleton. Although several studies have demonstrated the cellular heterogeneity of adult mature IVD, a single-cell transcriptomic atlas mapping early IVD formation is still lacking. Here, we generated the first spatiotemporal and single-cell based transcriptomic atlas of human IVD formation at embryonic stage, as well as a comparative mouse transcript landscape. The notochord (NC)/nucleus pulposus (NP) cells, vertebral chondrocytes, and annulus fibrosus (AF) cells were characterized. Our single-cell transcriptomic atlas that resolves spatiotemporally regulated cellular heterogeneity underlying early IVD development will be leveraged to develop preventative and regenerative strategies for IVD degeneration.
2025-10-25 | GSE216511 | GEO
Project description:We report the single-cell RNA-seq (scRNA-seq) data for human neonatal and adult human intervertebral disc (IVD) scRNA-seq. We sequenced cells harvested from three IVDs of a neonatal baby and one IVD from an adult cadaver.
2021-12-07 | GSE189916 | GEO